Example #1
0
        public float RunSiriusModel(string calibrationRoundID, string dataDirectory, string workDirectory, string projectDirectory, string genericAlgorithmsDirectory,
                                    ArrayList observationArray, ArrayList stdArray, int[] kParameterSiteIndex, int amplificationFactor, double CV, ArrayList observationDateArray, ArrayList observationSeperator)
        {
            #region Input variables
            //Assign the random values generated above to each of the parameters.

            int observationNumber = observationArray.Count;
            //Get the number of observations.

            string outputFileName      = "ModelOutput";
            string outputFileExtention = ".txt";
            string wholeOutputFileName = workDirectory + genericAlgorithmsDirectory + outputFileName + outputFileExtention;//Assign the path of the text file to save the model outputs concerned.
            File.WriteAllText(wholeOutputFileName, "");
            //Create a txt file to save model outputs concerned and clean up the output contents of last model run before a new run.
            #endregion

            #region Run the model
            AutomaticModelRun.ModelRun(
                TheArray,
                calibrationRoundID,
                dataDirectory,
                workDirectory,
                projectDirectory,
                wholeOutputFileName,
                kParameterSiteIndex,
                observationDateArray,
                observationSeperator
                );
            //Call the AutomaticModelRun statis class to run the model.
            #endregion

            #region Read model outputs
            List <double> modelOutputs    = new List <double>();
            StreamReader  SR              = File.OpenText(wholeOutputFileName);
            string        fileLineContent = null;

            modelOutputs.Clear();

            while ((fileLineContent = SR.ReadLine()) != null)
            {
                modelOutputs.Add(Convert.ToDouble(fileLineContent));
            }

            SR.Close();

            //Read the model outputs saved during the model run and save them in a list.
            #endregion

            #region Fitness calculation
            // fitness for the closest predictions to observations.

            predictionArray.Clear();

            for (int i = 0; i < observationNumber; i++)
            {
                predictionArray.Add(modelOutputs[i]);
            }
            //Prediction of anthesis dates and FLN of the hight nitrogen treatment at Clermont-Ferrand in 2007 and 2008 in order.
            //Declare an array to save the predictions concerned, e.g. anthesis date, final leaf number, LAI, etc.

            float[] fitnessValues  = new float[observationNumber];
            float   CurrentFitness = 1;

            for (int i = 0; i < observationNumber; i++)
            {
                double observationValue = Convert.ToDouble(observationArray[i]);
                double stdValue         = Convert.ToDouble(stdArray[i]);
                double predictionValue  = Convert.ToDouble(predictionArray[i]);
                //Console.WriteLine(amplificationFactor);

                if (observationValue != -999 & predictionValue != -999)
                {
                    //fitnessValues[i] = (float)(Math.Exp(-Math.Abs((float)Math.Pow((observationValue - predictionValue), 2) / (2 * (float)Math.Pow((stdValue* amplificationFactor), 2)))));
                    fitnessValues[i] = (float)(Math.Exp(-Math.Abs((float)Math.Pow((observationValue - predictionValue), 2) / (2 * (float)Math.Pow((observationValue * CV), 2))))) * amplificationFactor;
                    //The CV was modified to a variable for different sub-models since the fitness values are hard to calculate for many observation points.
                }
                else
                {
                    fitnessValues[i] = 1;
                }

                //Console.WriteLine("***");
                //Console.WriteLine(fitnessValues[i]);

                CurrentFitness = CurrentFitness * fitnessValues[i];
            }

            Console.WriteLine("The fitness value is {0}", Math.Round(CurrentFitness, 15));
            return(CurrentFitness);

            #endregion
        }
Example #2
0
        static void Main(string[] args)
        {
            Console.WriteLine("Global sensitivity analysis is starting, please wait...");//The procedure of GSA is starting.

            #region Working directory of the model.
            //int numberOfRandomLines = 860;
            //int numberOfParameters = 85; //For 85 parameters.

            int numberOfRandomLines = 770;
            int numberOfParameters  = 76;//For 76 parameters.

            string projectDirectory = @"C:\Postdoc Research\INRA\SiriusQuality1.5\Data\v1.5-Project\";
            string projectFileName  = @"v1.5-SensitivityAnalysis.sqpro";//The name of the run file of sensitivity analysis.
            string projectPath      = projectDirectory + projectFileName;
            //Console.WriteLine(projectPath);

            string GSADirectory = @"C:\Postdoc Research\INRA\SiriusQuality1.5\Data\INRA-BBSRC 16cv project\Sensitivity Analysis\";//GSA=global sensitivity analysis

            string inputDirectory = @"Morris\";
            //string RandomInputFileName = @"All Parameter-Morris-860.txt";
            string RandomInputFileName = @"76 Parameter-Morris.txt"; //It was changed to 76 parameters now.
            string RandomInputFilePath = GSADirectory + inputDirectory + RandomInputFileName;
            //Console.WriteLine(RandomInputFileName);

            string   outputDirectory     = @"Morris\";
            string   outputFileName      = "ModelOutput_Morris_";
            string[] treatmentNames      = new string[] { "AV-HighN", "AV-LowN", "CF-HighN", "CF-LowN", "RR-HighN", "RR-LowN" };
            string   outputFileExtention = ".txt";

            string[] wholeOutputFileNames = new string[treatmentNames.Length];

            for (int i = 0; i < wholeOutputFileNames.Length; i++)
            {
                string wholeOutputFileName = GSADirectory + outputDirectory + outputFileName + treatmentNames[i] + outputFileExtention; //Assign the path of the text file to save the temporary model outputs concerned.
                File.WriteAllText(wholeOutputFileName, "");                                                                             //Clear the temp ouput file that contains model outputs concerned.
                wholeOutputFileNames[i] = wholeOutputFileName;
                //Console.WriteLine(wholeOutputFileNames[i]);
            }
            #endregion

            ReadTextFile readTextFile = new ReadTextFile();
            string[,] randoms = readTextFile.ReadText(RandomInputFilePath, numberOfRandomLines, numberOfParameters); //Read the input file of random parameter sets.

            int usedRandomLines = randoms.GetLength(0);                                                              //The integer to show how many model runs will be conducted in current simulation.
            //int usedRandomLines = 200;

            for (int i = 0; i < usedRandomLines; i++)
            {
                #region 1. Load random parameter set.
                List <double> inputParameterValues = new List <double>();

                for (int j = 0; j < randoms.GetLength(1); j++)
                {
                    double temParameterValue = Convert.ToDouble(randoms[i, j]);
                    inputParameterValues.Add(temParameterValue);
                }
                #endregion

                #region 2. Run the model.
                AutomaticModelRun.ModelRun(inputParameterValues, GSADirectory, projectPath, wholeOutputFileNames);
                inputParameterValues.Clear();//Run the project.
                #endregion

                Console.WriteLine("Parameter set {0} is finished, please wait...", i + 1);
            }

            Console.WriteLine("Global Sensitivity Analysis is finished!");
            //Console.ReadLine();
        }